PDBsum entry 4cfh

Transferase

PDB id

4cfh

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Contents

			Protein chains

					402 a.a.


					69 a.a.


					21 a.a.


					301 a.a.

			Ligands

					STU


					AMP ×2

PDB id:

4cfh

Links

Name:

Transferase

Title:

Structure of an active form of mammalian ampk

Structure:

5'-amp-activated protein kinase catalytic subunit alpha-1. Chain: a. Fragment: residues 13-481. Synonym: ampk subunit alpha-1. Engineered: yes. Other_details: protease recognition sites were engineered into the alpha subunit at both ends of a large flexible loop in thE C-terminal region (residues 470 to 524), residues 471 to 523 were removed from the protein, residues 523 to 548 are given as chain c.

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562

Resolution:

3.24Å

R-factor:

0.234

R-free:

0.268

Authors:

B.Xiao,M.J.Sanders,E.Underwood,R.Heath,F.Mayer,D.Carmena,C.Jing, P.A.Walker,J.F.Eccleston,L.F.Haire,P.Saiu,S.A.Howell,R.Aasland, S.R.Martin,D.Carling,S.J.Gamblin

Key ref:

B.Xiao et al. (2011). Structure of mammalian AMPK and its regulation by ADP. Nature, 472, 230-233. PubMed id: 21399626

Date:

18-Nov-13

Release date:

25-Dec-13

Supersedes:

2y94

PROCHECK

	Headers

	References

Protein chain

P54645 (AAPK1_RAT) - 5'-AMP-activated protein kinase catalytic subunit alpha-1 from Rattus norvegicus

Seq: Struc:

Seq: Struc:					559 a.a. 402 a.a.*

Protein chain

O43741 (AAKB2_HUMAN) - 5'-AMP-activated protein kinase subunit beta-2 from Homo sapiens

Seq: Struc:					272 a.a. 69 a.a.

Protein chain

P54645 (AAPK1_RAT) - 5'-AMP-activated protein kinase catalytic subunit alpha-1 from Rattus norvegicus

Seq: Struc:

Seq: Struc:					559 a.a. 21 a.a.

Protein chain

P80385 (AAKG1_RAT) - 5'-AMP-activated protein kinase subunit gamma-1 from Rattus norvegicus

Seq: Struc:					330 a.a. 301 a.a.

Key:

Secondary structure

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class 1:

Chains A, C: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
2.	L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein]	+	ATP	=	O-phospho-L-seryl-[protein] Bound ligand (Het Group name = AMP) matches with 85.19% similarity	+	ADP	+	H(+)

L-threonyl-[protein]	+	ATP	=	O-phospho-L-threonyl-[protein] Bound ligand (Het Group name = AMP) matches with 85.19% similarity	+	ADP	+	H(+)

Enzyme class 2:

Chains A, C: E.C.2.7.11.26 - [tau protein] kinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	L-seryl-[tau protein] + ATP = O-phospho-L-seryl-[tau protein] + ADP + H⁺
2.	L-threonyl-[tau protein] + ATP = O-phospho-L-threonyl-[tau protein] + ADP + H⁺

L-seryl-[tau protein]	+	ATP	=	O-phospho-L-seryl-[tau protein] Bound ligand (Het Group name = AMP) matches with 85.19% similarity	+	ADP	+	H(+)

L-threonyl-[tau protein]	+	ATP	=	O-phospho-L-threonyl-[tau protein] Bound ligand (Het Group name = AMP) matches with 85.19% similarity	+	ADP	+	H(+)

Enzyme class 3:

Chains A, C: E.C.2.7.11.31 - [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ATP = O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ADP + H⁺

L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase]	+	ATP	=	O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] Bound ligand (Het Group name = AMP) matches with 85.19% similarity	+	ADP	+	H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Nature 472:230-233 (2011)
PubMed id: 21399626

Structure of mammalian AMPK and its regulation by ADP.
B.Xiao, M.J.Sanders, E.Underwood, R.Heath, F.V.Mayer, D.Carmena, C.Jing, P.A.Walker, J.F.Eccleston, L.F.Haire, P.Saiu, S.A.Howell, R.Aasland, S.R.Martin, D.Carling, S.J.Gamblin.

ABSTRACT

No abstract given.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22436748

D.G.Hardie, F.A.Ross, and S.A.Hawley (2012).
AMPK: a nutrient and energy sensor that maintains energy homeostasis.

Nat Rev Mol Cell Biol, 13, 251-262.

22659875

L.Chen, J.Wang, Y.Y.Zhang, S.F.Yan, D.Neumann, U.Schlattner, Z.X.Wang, and J.W.Wu (2012).
AMP-activated protein kinase undergoes nucleotide-dependent conformational changes.

Nat Struct Mol Biol, 19, 716-718.

PDB codes:

4eag 4eai 4eaj 4eak 4eal

22318606

Y.Y.Lin, S.Kiihl, Y.Suhail, S.Y.Liu, Y.H.Chou, Z.Kuang, J.Y.Lu, C.N.Khor, C.L.Lin, J.S.Bader, R.Irizarry, and J.D.Boeke (2012).
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.

Nature, 482, 251-255.

21490664

D.G.Hardie (2011).
Signal transduction: How cells sense energy.

Nature, 472, 176-177.

21892142

M.M.Mihaylova, and R.J.Shaw (2011).
The AMPK signalling pathway coordinates cell growth, autophagy and metabolism.

Nat Cell Biol, 13, 1016-1023.

21543851

N.Handa, T.Takagi, S.Saijo, S.Kishishita, D.Takaya, M.Toyama, T.Terada, M.Shirouzu, A.Suzuki, S.Lee, T.Yamauchi, M.Okada-Iwabu, M.Iwabu, T.Kadowaki, Y.Minokoshi, and S.Yokoyama (2011).
Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain.

Acta Crystallogr D Biol Crystallogr, 67, 480-487.

PDB codes:

2yza 3aqv

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.